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Run directory updates related to GEOS-IT #2153

Merged
merged 7 commits into from
Feb 16, 2024
Merged

Run directory updates related to GEOS-IT #2153

merged 7 commits into from
Feb 16, 2024

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lizziel
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@lizziel lizziel commented Feb 14, 2024 •
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Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

This PR contains several updates related to GEOS-IT meteorology and GCHP.

  • Added GEOS-IT processed lat-lon fields as a valid option when creating GCHP run directories. Previously these files were not available at WashU. Now there are at least a few days to test with.
  • Changed GCHP sample run scripts to not print script execution commands to log. This reduces the amount of output sent to log. The option is still present in the run scripts but is commented out. It can be uncommented to debug problems with the run script.
  • Changed offline emissions grid resolution templates in config files to be more descriptive. This applies to both GC-Classic and GCHP. It is a no-diff update but helps with clarify when reading the met files used to fill in HEMCO_Config.rc and ExtData.rc when creating a run directory. RUNDIR_MET_NATIVE_RES is now RUNDIR_OFFLINE_EMIS_RES and RUNDIR_MET_LAT_RES is now RUNDIR_OFFLINE_EMIS_LAT_RES. Entry RUNDIR_MET_LON_RES is deleted since it is not used.
  • Fixed GEOS-IT native lat-lon filenames used for clusters other than discover. This now enables GCHP run directories using GEOS-IT native lat-lon meteorology to work.
  • Fixed offline emission paths set when using GEOS-IT meteorology. This now enables GCHP standard simulations using GEOS-IT meteorology to run. Previously they failed due to incorrect population of the offline emission paths in ExtData.rc.

Expected changes

This is a zero diff update

Related Github Issue(s)

closes geoschem/GCHP#379

@lizziel lizziel added topic: GCHP Related to GCHP only topic: Configuration Files Related to GEOS-Chem configuration files no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations category: Bug Fix Fixes a previously-reported bug labels Feb 14, 2024
@lizziel
Fix GEOS-IT native lat-lon filenames used in GCHP ExtData.rc
8e3c88e 
File had discover cluster file format instead of file format available
at WashU.

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel
Rename rundir creation variables used for offline emissions grid res
0b54176 
- RUNDIR_MET_NATIVE_RES is now RUNDIR_OFFLINE_EMIS_RES
- RUNDIR_MET_LAT_RES is now RUNDIR_OFFLINE_EMIS_LAT_RES
- Deleted RUNDIR_MET_LON_RES since not used
- All relevant template files are also updated

This update also fixes a bug when using native cubed-sphere GEOS-IT
meteorology which caused the offline emissions paths in ExtData.rc
to be wrong.

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel
Update GCHP run scripts to not print all run script commands
db95454 
The option to print all run script commands is commented out as a debug
option. Having it on by default clutters the GCHP log file.

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel
Update GCHP rundir options to include using pre-processed GEOS-IT lat…
45e65d8 
…-lon

These files are still being generated at WashU but there are now at least
a few dates to run with.

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel
Updated changelog
d1b4d18 
Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel lizziel marked this pull request as ready for review February 14, 2024 22:27
@lizziel lizziel changed the base branch from main to dev/no-diff-to-benchmark February 14, 2024 22:27
@yantosca yantosca self-assigned this Feb 15, 2024
@yantosca yantosca self-requested a review February 15, 2024 14:44
yantosca
yantosca requested changes Feb 15, 2024
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@lizziel: Just needs a changelog entry and then it's good to merge. Thanks for this!

run/shared/settings/geosit/geosit.native_ll.txt Show resolved Hide resolved
@yantosca yantosca self-requested a review February 15, 2024 18:38
yantosca added a commit that referenced this pull request Feb 15, 2024
@yantosca
Add changelog update for PR #2153
f596c9f 
CHANGELOG.md
- Add note about fixes for GEOS-IT rundir creation

Signed-off-by: Bob Yantosca <[email protected]>
yantosca
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@lizziel: I pushed the changelog update. Now moving to integration tests

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lizziel commented Feb 15, 2024

Oops, forgot the changelog again! I'm going to push an update on top of yours for the changelog.

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lizziel commented Feb 15, 2024

I can fix the conflicts too

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lizziel commented Feb 15, 2024

Looks like I already did a changelog but just forgot to push. I will fix the branch.

@lizziel lizziel force-pushed the bugfix/geosit_rundir_creation branch from f596c9f to d1b4d18 Compare February 15, 2024 19:03
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lizziel commented Feb 15, 2024

All set now. I had rebased on dev/no-diff-to-benchmark but forgot to push that too. This PR now has my changelog updates and no conflicts with dev/no-diff-to-benchmark.

@yantosca
Bug fix: Now use RUNDIR_OFFLINE_{NATIVE,LAT}_RES in HEMCO templates
35a5708 
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- Replace RUNDIR_MET_NATIVE_RES with RUNDIR_OFFLINE_EMIS_RES
- Replace RUNDIR_MET_NATIVE_LAT with RUNDIR_OFFLINE_EMIS_LAT_RES

run/shared/settings/merra2
- Add RUNDIR_OFFLINE_EMIS_RES and RUNDIR_OFFLINE_EMIS_LAT_RES

Signed-off-by: Bob Yantosca <[email protected]>
yantosca
yantosca approved these changes Feb 16, 2024
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I've pushed a change to make sure that RUNDIR_OFFLINE_EMIS_RES and RUNDIR_OFFLINE_EMIS_LAT_RES are defined for MERRA-2 meteorology. Also the GCHP and GCClassic HEMCO_Config.rc.fullchem template files needed to be updated to replace RUNDIR_MET_NATIVE_RES with RUNDIR_OFFLINE_EMIS_RES and RUNDIR_MET_LAT_RES with RUNDIR_OFFLINE_EMIS_LAT_RES.

@yantosca
Fix typo in BIOGENIC_MTPA entry in HEMCO_Config.rc.fullchem
788d8e4 
run/GCClassic/HEMCO/HEMCO_Config.rc.fullchem
- In the entry for BIOGENIC_MTPA for OFFLINE_BIOGENICVOC, we have fixed
  a typo: RUN_MET_OFFLINE_RES -> RUNDIR_OFFLINE_EMIS_LAT_RES.  This
  was causing GCClassic fullchem integration tests to fail

Signed-off-by: Bob Yantosca <[email protected]>
@yantosca yantosca merged commit 8470181 into dev/no-diff-to-benchmark Feb 16, 2024
@yantosca yantosca added this to the 14.3.1 milestone Feb 16, 2024
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All GCClassic and GCHP integration tests passed.

All GCHP integration tests were zero-diff w/r/t 14.3.0. All GCClassic integration tests were zero-diff w/r/t 14.3.0, except:

  • APM (known parallelization issue)
  • RRTMG (numerical noise in RRTMG diagnostic collection output)

@yantosca yantosca deleted the bugfix/geosit_rundir_creation branch March 5, 2024 20:37
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category: Bug Fix Fixes a previously-reported bug no-diff-to-benchmark This update will not change the results of fullchem benchmark simulations topic: Configuration Files Related to GEOS-Chem configuration files topic: GCHP Related to GCHP only
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GEOS-IT ExtData reading error and debugging
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@lizziel @yantosca